Abstract Background Autonomy is recognized as important for individual well-being and constitutes one dimension in the KIDSCREEN-instrument measuring health related quality of life (HRQoL) in children and adolescents. However, the autonomy questions in KIDSCREEN are restricted to opportunities to influence leisure time activities, which is a form of autonomy as volition. Yet, there are other aspects of autonomy that might be related to adolescent’s HRQoL. The aims of the present study were first to investigate the psychometric properties of a scale measuring autonomy in adolescence from a control perspective (AAC) including its relation to the autonomy dimension in KIDSCREEN, and second; to investigate AACs ability to predict each of the 10 dimensions constituting KIDSCREEN. Methods Students (n = 154) aged 15–16 years who were recruited from schools located in both low (two schools) and high (two schools) socioeconomic status (SES) areas in Sweden participated in a cross-sectional study. The adolescents answered a questionnaire including a new 6-item scale measuring perceived autonomy and HRQoL assessed by the KIDSCREEN-52 instrument. A factor analyses was computed to investigate the relation between the items in the AAC scale and the autonomy items in the KIDSCREEN instrument. Hierarchical regression analyses were computed to investigate if the AAC scale predicted HRQoL in any of the 10 dimensions in KIDSCREEN after controlling for gender, SES and the original autonomy scale included in KIDSCREEN. Results The factor analysis showed that all the items from the autonomy scale loaded in one factor and that all the items from the AAC scale loaded in another dimension. The hierarchical regression models showed that the AAC scale uniquely predicted HRQoL in all dimensions of the KIDSCREEN instrument after controlling for gender, SES and the original autonomy scale included in KIDSCREEN-52. A high level of perceived autonomy was associated with a high level of HRQoL for both scales. Conclusion A new scale for measuring autonomy from a control perspective has been presented and shown to differ from autonomy as volition. Both forms of autonomy are positively related to HRQoL in adolescence 15–16 years old.